On Sat, Jul 24, 2010 at 3:39 PM, Jonathan Tu <j...@princeton.edu> wrote: > > On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote: > >> On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu <j...@princeton.edu> wrote: >> >>> >>> What does that part do? It turns out that by fixing my library path, numpy >>> now imports. I assume that my installation of h5py doesn't need to be >>> redone just because I reinstalled Numpy? >> >> Actually, you may have to if you installed h5py against the numpy >> built from the trunk. I don't think the trunk ABI is forward >> compatible with 1.4.1, >> >> David > > > Ok, so I reinstalled numpy as we've discussed, and now I've reinstalled h5py > too. When I test numpy, I get the following > > import numpy > numpy.test() > Running unit tests for numpy > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", > line 326, in test > self._show_system_info() > File > "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", > line 187, in _show_system_info > nose = import_nose() > File > "/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py", > line 69, in import_nose > raise ImportError(msg) > ImportError: Need nose >= 0.10.0 for tests - see > http://somethingaboutorange.com/mrl/projects/nose > > Note that when I try test(level=1) it tells me this is an unexpected keyword > argument. (The level=1 was suggested by the scipy website.) Though this > test seems to fail, the simple math tests I've tried seem to work ok. > > Then I tried to test h5py: > import h5py > import h5py.tests > h5py.tests.runtests() > > ====================================================================== > ERROR: test_data (h5py.tests.test_filters.TestFilters) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", > line 124, in test_data > test_dset(s, t, compression=c, shuffle=False) > File > "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py", > line 117, in test_dset > dset[...] = arr > File "/home/jhtu/local/lib/python2.6/site-packages/h5py/highlevel.py", line > 1288, in __setitem__ > self.id.write(mspace, fspace, val, mtype) > File "h5d.pyx", line 231, in h5py.h5d.DatasetID.write (h5py/h5d.c:2336) > File "_proxy.pyx", line 115, in h5py._proxy.dset_rw (h5py/_proxy.c:1143) > TypeError: Not a dataset (Invalid arguments to routine: Inappropriate type) > > ====================================================================== > FAIL: (File) Backing store for core driver > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", > line 135, in test_backing > self.assert_('g' in self.f) > AssertionError > > ====================================================================== > FAIL: (File) Append > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", > line 52, in test_a > self.assert_('g' in self.f) > AssertionError > > ====================================================================== > FAIL: (File) Readwrite > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py", > line 72, in test_rp > self.assert_('g' in self.f) > AssertionError > > ====================================================================== > FAIL: test_open_close (h5py.tests.test_h5g.TestH5G) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_h5g.py", > line 39, in test_open_close > self.assert_(self.is_grp(grp)) > AssertionError > > ---------------------------------------------------------------------- > Ran 247 tests in 1.307s > > FAILED (failures=4, errors=1) > <unittest._TextTestResult run=247 errors=1 failures=4> > > > But again, I seem to be able to open hdf5 files and look into them ok, though > sometimes the files randomly close, i.e. > > f = h5py.File( '/path/to/file.h5','r') > ... > f > <Closed hdf5 file> (or something like this) > > Should I be worried about these errors, or are things working ok? Someone > had once mentioned to me that the numpy tests are prone to failure. > >
Yes, you should be worried. To run the numpy tests you need to install nose. That's what your output said: ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose For h5py, you might want to try the h5py list. Did you remove the build directory? Because I don't know much about installation, I remove everything: the installed package, the build directory. _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion